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Add the predicted value of EVE for each variant.

EVE_Final.Rd

Add the predicted value of EVE for each variant in "gene name_Target or Pathogenic_finalpredict.csv".

Usage

EVE_Final(file_name, EVE_file_name)

Arguments

file_name

Path to "gene name_Target or Pathogenic_finalpredict.csv" file output by the MOVA function

EVE_file_name

EVE variant files for targeted genes. These files are available at https://evemodel.org/.

Details

Value

References

Author

Yuya Hatano

Note

See also

Examples

Hgmd_divide("./source/TARDBP.csv")
Edit_gnomAD_file("./source/gnomAD_v3.1.2_ENST00000240185_2023_02_14_13_23_48.csv", "./source/TARDBP_gnomAD.csv")
Edit_variant_data("../CADD_REVEL/AlphScore_final.tsv", "./source/TARDBP.csv", "./source/TARDBP_gnomAD.csv", "Q13148", "TARDBP", "./source/TARDBPvariantdata.csv")
Edit_polyphen_data("../dbNSFP/dbNSFP4.3a/dbNSFP4.3a_variant.chr1","./source/TARDBPvariantdata.csv", "TARDBP_alph.csv",  "Q13148",  11012654, 11025492 ,"./source/TARDBPvariantdatapol.csv", "./source/TARDBP_alphpol.csv")
Edit_final_variant_file("./source/TARDBP_alphpol.csv","./source/TARDBP_alphpol2.csv")
MOVA("./source/Q13148.fa", "TARDBP", "./source/AF-Q13148-F1-model_v2.pdb","./source/TARDBP_alphpol2.csv", "./source/TARDBPvariantdatapol.csv")
EVE_Final("TARDBP_Target_finalpredict.csv", "../dementia/EVE_all_data/variant_files/TADBP_HUMAN.csv")

## The function is currently defined as
function (file_name, EVE_file_name) 
{
    df <- fread(file_name)
    y <- fread(EVE_file_name)
    df[, `:=`(EVE, NA)]
    df[, `:=`(EVE_class, NA)]
    df$Pos <- as.integer(substr(df$change, 2, nchar(df$change) - 
        1))
    for (i in 1:nrow(df)) {
        df$EVE[i] <- y[(y$position == df$Pos[i]) & (y$mt_aa == 
            df$aaalt[i])]$EVE_scores_ASM
        df$EVE_class[i] <- y[(y$position == df$Pos[i]) & (y$mt_aa == 
            df$aaalt[i])]$EVE_classes_75_pct_retained_ASM
    }
    fwrite(df, file_name)
  }
#> function (file_name, EVE_file_name) 
#> {
#>     df <- fread(file_name)
#>     y <- fread(EVE_file_name)
#>     df[, `:=`(EVE, NA)]
#>     df[, `:=`(EVE_class, NA)]
#>     df$Pos <- as.integer(substr(df$change, 2, nchar(df$change) - 
#>         1))
#>     for (i in 1:nrow(df)) {
#>         df$EVE[i] <- y[(y$position == df$Pos[i]) & (y$mt_aa == 
#>             df$aaalt[i])]$EVE_scores_ASM
#>         df$EVE_class[i] <- y[(y$position == df$Pos[i]) & (y$mt_aa == 
#>             df$aaalt[i])]$EVE_classes_75_pct_retained_ASM
#>     }
#>     fwrite(df, file_name)
#>   }
#> <environment: 0x0000011a8b791880>